Over the past year, emerging variants have changed the calculation of the pandemic, forcing countries to fall back on them and reconsider their vaccine strategies. Essentially, it’s now a race: Getting photos for more people will help calm the spread of variants and slow the emergence of new ones. But in Africa, where only a few countries have so far received a net of vaccines, this process should take longer. And as the virus continues to replicate and spread among people, it will also continue to change – with implications for the entire world.
“It’s going to be bumpy,” says Christian Happi, director of ACEGIP. “On the continent we have found a number of major variants, and there are probably many more.” It is not uncommon for African states to work together to quell epidemics, he notes. Not all countries have access to the sequencing machines that quickly analyze these genomes, and those that do so often depend on a single commercial laboratory. So governments and labs have learned to collaborate, forming networks that use advanced sequencing centers like hers and de Oliveira to fight emerging diseases, rather than sending samples overseas. So far, in 2021, the initiative has helped double the number of viral genomes sequenced in Africa compared to 2020, with a goal of producing 50,000 genomes by the end of the year.
Even as the ability to sequence increases, the process remains difficult, says Happi. A high rate of asymptomatic cases and limited access to healthcare means Covid-19 tests that lead to genome sequencing are limited in some areas. And it is not easy to collect and store samples from a country like Somalia and send them to Nigeria, via multiple planes and handlers, while keeping them perfectly intact. From a few hundred samples in a recent delivery from Mogadishu, the lab has recovered full sequences of just 10 of them.
One way to think about the variants of SARS-CoV-2 is a series of epidemics within the pandemic. When the variants emerge first, or when they first arrive in a new place, they are like embers, ready to catch fire if the opportunity to spread presents itself and if their mutations make them competitive with other strains. But embers are also easier to put out than widespread fires. Variants can be stopped at borders, and outbreaks in hot spots can be identified and canceled – provided Variant Hunters move fast and throw a wide net. “We need a consistent and fast rotation because these variations tend to dominate quickly,” says de Oliveira. “You don’t want to find out six months late that you have an epidemic of a strain that escapes the vaccine.”
The type of border checks carried out in Angola, in response to surges linked to variants found in neighboring countries, is a good example of surveillance implementation, de Oliveira says. Samples from the airport revealed not only the new strain, but numerous examples of B.1.351 and B.1.1.7, the variants of concern first identified in South Africa and the UK and now circulating. in the whole world. He believes the early detection of such cases is a crucial part of why Angola did not experience the same outbreak as its neighbors earlier this year. Monitoring of travel centers also increases overall coverage; researchers had no way of doing genomic surveillance in Tanzania, for example, until these three travelers arrived during border control.
Even when worrisome variations set in, the ability to track them has an impact on the public health actions officials can take. “Sequencing really helps because you understand the human migration patterns for a variant,” Happi says. In Nigeria this winter, for example, the government worried about a power surge of unknown origin. It was impossible at first to tell if the virus was spreading faster or if human behavior was the cause. Genome sequencing revealed he was driven by B.1.1.7, the variant that was first identified in the UK, allowing health officials to identify hot spots and, most importantly, d ‘explain to the audience why it was necessary to curl up. Likewise, when researchers at the Uganda Virus Research Institute identified a new variant circulating there, the surveillance led to more testing in prisons and on truck routes across the country, where the tension was most concentrated.